The UN special envoy to Afghanistan, Kai Eide, admitted at the weekend that there had been widespread fraud in the presidential election. Photograph: OMAR SOBHANI/REUTERS

A member of a UN-backed panel set up to investigate complaints of fraud in Afghanistan's presidential election resigned today, blaming the "interference of foreigners", in a setback to attempts to restore legitimacy to the electoral process.

Maulavi Mustafa Barakzia, one of only two Afghans on the Electoral Complaints Commission, claimed that the three foreigners on the panel – one Canadian, one Dutch and one from the US – were "making all decisions on their own" without consultation.

The panel is expected to decide this week how many votes to throw out, a decision that could force a run-off between President Hamid Karzai and his closest challenger, Abdullah Abdullah.

A UN spokesman, Aleem Siddique, said the resignation was "regrettable but the work of the Election Complaints Commission must continue. The Afghan people need to see an election outcome that faithfully reflects their will as soon as possible."

Eide's deputy, Peter Galbraith, the top-ranking American in the UN mission, was sacked last month after alleging that the mission chief played down allegations of widespread ballot-stuffing by Karzai's supporters.

US relations with Karzai, already frosty before the poll because of widespread allegations of corruption, have been further strained by claims of vote rigging.

The US secretary of state, Hillary Clinton, said today Karzai had been "very helpful on many fronts", and progress in Afghanistan was often "overlooked". But she said that if he were returned to office, there would have to be "a new relationship" between Karzai and foreign governments.

Clinton, who is visiting Britain, also said the Obama administration was reassessing the relationship between the Taliban and al-Qaida, but denied any change of strategy on Afghanistan had occurred.

Her comments came after reports that the president's security advisers were pressing him to shift the focus of the war from the Taliban in Afghanistan to al-Qaida in Pakistan. The Taliban issued a statement last week claiming they posed no international threat, in an apparent attempt to put daylight between themselves and al-Qaida.

Asked whether the US was changing its focus, Clinton told BBC Radio 4's Today programme: "We are not changing our strategy: our strategy remains to achieve the goal of disrupting, dismantling and defeating al-Qaida and its extremist allies and denying them safe haven and the chance to strike us here in London, in New York and anywhere else."

But she added: "We are doing a much more careful analysis of who is actually allied with al-Qaida. Not everyone who calls himself a Taliban is necessarily a threat to the UK or the US."

Clinton said the US was learning from its experiences in Iraq, where people may have been "coerced or intimidated" into fighting alongside al-Qaida. The US had approached those people and persuaded them to change sides.

"There may well be a number of people currently who are considered Taliban who are there, frankly, because they get paid to fight or because they see no alternative," she said.

Public opinion against the war in Afghanistan has intensified in the US in recent months as the death toll of US troops has mounted. Obama's apparent reluctance to provide more soldiers, as requested by General Stanley McChrystal, commander of US and Nato forces in Afghanistan, has been interpreted in some quarters as a sign of a wavering commitment to the conflict.

Clinton said: "You should never doubt our commitment or our leadership. We will not rest until we do defeat al-Qaida, but we want to be smart about how we are proceeding."